I loved the good old fashioned sword fight in Twilight Princess. It was epicly done with the Twilight Barrier around you and Zelda being just outside, only able to watch.
My personal favorite was OoT Ganon, because OoT's Ganondorf/Ganon is the only Ganon fight i've ever gotten to, and Ganondorf wasn't hard, just mildly annoying. Not that Ganon was much harder.